/r/Biochemistry

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A place to post news and discuss the frontiers of biochemistry and biotechnology. Please refrain from posting home videos with songs and raps.

/r/Biochemistry

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0

Looking for a Collab Biochemist , For a new Assay Development

I am hereby looking forward to Collab with seniors/ juniors all round the world to develop an assay which essentially removes haemolysis ( in specimens recieved during pre- analytical phase). Note that we can file PCT application later collaboratively. Given that resources are within the laboratory reach of limits and no ethical boundaries for this assay development. And another assay to remove lipemia, such as using PEG which is already established, however modification will develop a new Assay which removes the interferences. PEG generally clears the sample for easier detection of SGOT & SGPT ALP. Along side any devices available within your laboratory capacity to remove such interferences are hugely welcome to contribute your views here Thanks and regards

0 Comments
2024/06/30
13:27 UTC

1

Masking reagent

what reagent is used to mask LDL-C from HDL, VLDL in serum in order at the end to determine the cholesterine concentration?

0 Comments
2024/06/30
10:40 UTC

173

I’ve been cloning for 5 years, 2000+ constructs, Ask me anything

Ask me all your cloning and synthetic biology questions and I’ll do my best to answer them.

Qualifications:

Current grad student at a top 10 program in US, Prior research tech at MSKCC, Synthetic Biology Enthusiast

Edit: ask me anything about cloning. Want to share the wealth of knowledge, not intended to be a flex thread as a few people have mentioned.

121 Comments
2024/06/29
20:23 UTC

2

Can anyone clarify the concept of receptor sensitivity and how it can change?

It would be very helpful if someone explains it or send articles regarding that. I could only find one article, and it was helpful but not that much that I understand that clearly.

Thanks.

0 Comments
2024/06/29
10:11 UTC

19

Great books for lifelong learning?

I recently graduated with a degree in Biochemistry. Although I’m not planning to pursue a Master’s degree, I still want to continue learning Biochemistry both for personal interest and career purposes.

I have a copy of "Fundamentals of Biochemistry" by Voet & Voet, and I've memorized almost all the details in it, thanks in part to my research lab work that requires a solid understanding of the fundamentals. While it’s an amazing book, I'm now looking for a concise, handy reference that I can quickly grab and use for self-learning. Do you have any suggestions for such books?

I’d prefer something small in size (rather than a full textbook size of a Lehninger or Voet), and summarized yet detailed enough to be helpful for research references.

4 Comments
2024/06/29
07:01 UTC

1

Jun 29: Cool Papers

Have you read a cool paper recently that you want to discuss?

Do you have a paper that's been in your in your "to read" pile that you think other people might be interested in?

Have you recently published something you want to brag on?

Share them here and get the discussion started!

0 Comments
2024/06/29
00:00 UTC

1

Filtering commercial enzyme powders reduced efficacy?

We are doing biodegradation studies in a-galactosidase. For pilot tests, we are just using Target brand generic Beano (link). Seems like, as compared to the buffer only control, the a-galactosidase does degrade our substrate when using the powder directly from the capsule.

A student brought up the concern that the solids in the powder could be physically battering the substrate when being stirred in the beaker.

To assuage this concern, we filtered the powder through a 0.2um PES filter disc. We then noticed that the effect is dampened. Is there a chance that the enzyme is actually bound to the solids and we are filtering a majority of it out?

1 Comment
2024/06/28
22:49 UTC

2

Rosetta fold all atom

Hi guys, I couldn't set up RFAA on my computer, that is why, I am using tamarindbio website to test some structures on RFAA. However, it limits the length of the amino acids up to 700, so I cannot put there most of the structures that I want. I want to see if RFAA predict 8FLW ( antibody-virus envelope complex) right because alphafold3 cannot do it. Please someone help me on this, I would really appreciate it if someone does it and send me the result. Thank you in advance! Note: I am just doing it to learn!!!

5 Comments
2024/06/28
21:12 UTC

6

Eukaryotic Translation

One of the most difficult topics to remember in depth when I took biochemistry 2 for undergrad was eukaryotic translation. This involves all the factors involved for each step, as well as the details of what each factor does and the overall process that occurs. I found it extremely difficult to remember these, especially the details for the elongation factors. What are some tips and tricks you guys used to memorize these down to every single detail, sentence, and word? Thank you :)

2 Comments
2024/06/28
18:53 UTC

2

ChimeraX or PyMOL?

I'm curious to get a general view of what software y'all prefer to use for visualizing and making figures of protein structures. If you use both, I'd love to hear which software you prefer for what functions! I personally prefer ChimeraX; I know PyMOL has its fans, but my experience with PyMOL is limited, and I've gotten used to ChimeraX's commands and interface. Love to hear from you all!

View Poll

2 Comments
2024/06/28
16:18 UTC

7

Uses of a Biochem degree?

I’m looking to get some advice on what types of work a biochem degree can get you straight out of college. Most online sources only talk about medical related jobs, but I’m not interested in going to medical school. I really enjoy chemistry in general (ochem was my favorite so far), and plan on taking infectious disease bio classes and working in research labs at my uni. As someone who can relocate anywhere, will it be challenging to find a job after undergrad and what types of industries could I find work in as a new graduate?

8 Comments
2024/06/28
08:00 UTC

0

PCR RUN HELP

I have attached A photo of my PCR run for a plasmid that is about 9kb. Lane 1 is my ladder and lane 4 and 5 are my controls. Lane 5 is the stock plasmid and lane 4 is my plasmid I purified from e-coli. Why does my purified plasmid appear to have two bands at the expected 9kb while the original stock plasmid has the expected 1 band? Also, during my second run today, my PCR rxn (lane 2) seems to not generate a complete length plasmid (around 9kb) and I keep getting a dense band at 3kb.. (same band as lane 2). Why is this ? If this is due to dNTP concentrations shouldnt i still get a hand at 9kb?

10 Comments
2024/06/28
04:25 UTC

13

PCR works, but mostly at a completely wrong size

I've been trying to clone out a gene from a plasmid stored in DH5-alpha. Purified out the plasmid with Qiagen miniprep, then ran pcr with primers based (from nebcalc) designed from the supposed sequence of the plasmid. PCR ran with Q5 polymerase.

However, DNA gel of results shows a very strong (no/little smearing) band at a fragment size nearly 1kb larger than my target gene (~2100 vs ~900bp). There's also a much fainter band of my target gene at the correct size.

I have no idea what's going on. I rechecked the plasmid to see if my primers are binding to other places, and it doesn't seem like it. I also considered DNA secondary structure messing with the gel, but I think that would result in more smearing. The only thing I can think of is that the ordered plasmid is just wrong, but there is a weaker band at the expected size...

28 Comments
2024/06/27
19:06 UTC

2

How to disimpact a 1/8 ss coil?

Been dealing with a 1/8 stainless coil that is impacted with what can only be biofilm.

Tried boiling it in water, soaking in 2% detergent, bath sonicating, ethanol bath.

I'm afraid to use HCl or other reducing acids for fear or corrosion.

Any suggestions outside of replacing the coil?

5 Comments
2024/06/27
18:08 UTC

4

Need Advice on Choosing Between Biochemistry and Chemical Engineering at ETH Zurich

Hi everyone,

I’m reaching out for some advice on choosing between Biochemistry and Chemical Engineering for my studies at ETH Zurich. I’m torn between these two fields and could really use some insights from those who have experience or knowledge in these areas.

Here’s what I like about both:

1.	Biochemistry:
•	I believe it’s more research-focused.
•	It seems to delve deeper into biological systems, which I find fascinating.
•	I have a strong interest in pursuing research, possibly aiming for a role like Chief Scientist in the future.
•	Starting a biotech startup is also a long-term goal of mine.
2.	Chemical Engineering:
•	I like the technical and industrial orientation of this field.
•	It’s not limited to biological systems but also includes biofuels, new energy sources, and other innovative technologies, which I find very appealing.
•	I’m interested in working on an industrial scale and eventually taking on a leadership role in a company.

My main questions are:

•	How research-oriented is Chemical Engineering compared to Biochemistry? Are there many opportunities to end up in research roles as a Chemical Engineer?
•	Are there examples of Chemical Engineers who have successfully transitioned into research or started their own biotech companies?
•	For my career goals (Chief Scientist, biotech startup), which bachelor’s degree would be more beneficial?
•	After the bachelor’s, would it be better to pursue a master’s in Biotechnology, Biochemical Engineering, or something else like Biomedical Engineering or Chemical and Bioengineering?
•	How can each path contribute to achieving my career aspirations?

I’m planning to make this decision with the goal of eventually being in a significant research or leadership position, preferably in the biotech industry. Any advice, personal experiences, or insights would be greatly appreciated!

Thanks in advance for your help!

2 Comments
2024/06/27
09:02 UTC

1

How to calculate enzyme specific activity ?

I performed an endocellulase activity assay using a beta-glucan substrate and utilized 50 ng of enzyme for the activity assay. The absorbance was measured at 575 nm. Now, I need to calculate the enzyme's specific activity from this step, as I only have the absorbance value. Could anyone assist me in calculating this? Please, it's an emergency. help me.

3 Comments
2024/06/27
07:21 UTC

2

Conservation Biology vs. Biochemistry?

Hello everyone! I am currently a conservation biology major going into my junior year of university. My dream career is to work in a research lab focusing on solutions to climate change and its effects. I plan on getting my masters after my undergrad and possibly getting my phD. I have found that I have enjoyed my chemistry classes more than my biology classes, and I am especially interested when I hear about what people learn in biochemistry class and the two subjects combine. I have been considering changing my major to biochemistry, because I want to work in a lab setting, I find the subject interesting, and I have heard good things about job opportunities with biochem. My main problem is that I am worried if I switch to biochem, I will be straying away too far from conservation and I won’t be able to get jobs or internships that are surrounding climate change and environmental science. Would it be beneficial switching to biochemistry or would it hurt me in the long run because it is not as focused on conservation? Any advice/opinions are appreciated. Thank you!

3 Comments
2024/06/26
23:47 UTC

8

Gluconeogenesis from Glutamine

Hey guys! I'm studying Biochemistry for my finals and I have this question to which I cannot find an answer. Glutamine becomes glutammate and then Alpha keto glutarate that enter the Krebs Cycle. In the end, oxalacetate is produced and it will become phosphoenolpyruvate and eventually glucose. My question is: how does oxalacetate exit the mitochondria? Via the malate aspartate shuttle? Or returning malate via malate dehydrogenase? I'm quite sure that oxalacetate becomes Phosphoenolpyruvate in the citosol and not in the mitochondria itself (like it happens when considering gluconeogenesis from lactate). Please help me! And sorry for my bad English, I'm not a native speaker. Thank u :)

7 Comments
2024/06/26
18:31 UTC

2

Jun 26: Education & Career Questions

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

2 Comments
2024/06/26
15:01 UTC

1

Help with some key concepts

I recently came into an opportunity where suddenly I’m hearing all sorts of terms like mRNA and pre-mRNA and NMR and alternate splicing and exons and introns and I’m honestly nowhere near that level at the moment so I was hoping that maybe someone on here who understands them could explain like I’m 5? Lol thank you

4 Comments
2024/06/26
08:32 UTC

1

Incoming Biochem student

Good afternoon Everyone,

I’m a incoming biochemistry student for the fall term and my goal at the end of the 4 years is to pursue dentistry. I’ve currently just chose my classes and they recommend to switch to Biology BA major due to less chem classes and less math which they stated Biochemistry is more focused if you wanna do something in chemistry or lab. How’s the work force and is the money good obtaining a degree in biochemistry towards wanting to become a dentist in the future. What will be the best route to open more doors in the future.

6 Comments
2024/06/25
19:18 UTC

1

Ligand receptor interaction and the concept of dissociation constant

Can anyone please introduce me a book about the title's context I mentioned ?

I am really confused about this, as I am reading articles.

12 Comments
2024/06/25
17:39 UTC

26

Is academia really that bad how people tell on social media ? Am I making a mistake ?

I hope one day my research could be applied into medicine. Was thinking of doing my bachelor's in bio-medical. Intererest lies in immunology/pathogen interaction/drug interaction inside the human body

  1. I have read how the pay in academia is very low and often people advicing not to pursue it. Is this really true ?

(I belong from not a well-to-do family and pay is a factor for me. And hope I can help my family)

  1. do researchers even at premier institutions do not get good pay ? PhD stipend ? Even after we work hard ? Professors at leading institutes ?

  2. how much is the difference in pay in industry vs academia ( top position) and can one pursue independent research while being in industry ?

Pardon if my wordings are incorrect, I don't have any guide and all this is very new to me.

22 Comments
2024/06/25
16:28 UTC

2

Problem-based learning for someone thinking of going back to school?

Haven't done any edu-mah-cation since high school, but I've been thinking of going back, after learning a bit about things like synthetic, micro-, and molecular biology. Before deciding whether this kinda of investment of time & treasure is a good idea, I've been looking into what to learn, which led me down a rabbit hole of how to learn. On the one hand it's almost silly, but on the other - Kerbal Space Program.

I like the approach these two articles push:

Obviously, there'll only be so much I can do without a lab, mentorship, and so on. But like I said, going back to school in my mid-twenties while supporting a family is a big decision, and I wanna see whether I'd be a good fit for it. So, past picking up the latest copy of Campbell and working through that, what are some good books for learning through problems you'd recommend? The little research I've done (cause I admit I'm not slick enough to assess quality learning materials, as a layman) has me thinking that Cell Biology by the Numbers would be a good fit. Apparently Molecular Biology of the Cell is also a good book, but with problems that aren't as good as CBbtN's.

0 Comments
2024/06/25
06:23 UTC

1

Jun 24: Weekly Research Plans

Writing a paper?

Re-running an experiment for the 18th time hoping you finally get results?

Analyzing some really cool data?

Start off your week by sharing your plans with the rest of us. å

0 Comments
2024/06/24
15:00 UTC

298

We've all been there

10 Comments
2024/06/24
12:35 UTC

1

How to color different domains of a protein using Pymol? (Publication quality)

Checkout this interesting video that demonstrates the conversion of default boring representation of DNA to more informative and publication ready image to use in your scientific literature.

The following structure is of FMN riboswitch that has 6 stem and 5 loop structure. Each loop and stem is represented in a distinct color.

This tutorial demonstrates the step by step guide for replicating such representation for your proteins as well!

0 Comments
2024/06/24
03:50 UTC

8

Question About Nickel

I see a lot of information advising that people with a nickel allergy avoid different cosmetic ingredients & food products. For example, soy lecithin C42H80NO8P. However, this does not contain "Ni". If there is not actually Nickel within the chemical formula for a product or ingredient, how can it be something that is reactive for people with a Nickel allergy. What am I missing? (I am not a biochemist, I just enjoyed biochemistry in school & am trying to use logic & reason to sort through garbage information.). Thank you!

4 Comments
2024/06/23
21:34 UTC

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